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Zika NS3 helicase:RNA complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JLQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% (w/v) ethylene glycol, 10% (w/v) polyethylene glycol 8000, 0.1 M MES/Imidazole pH 6.5, 20mM sodium formate, 20mM ammonium acetate, 20mM tri-sodium citrate, 20mM sodium potassium L-tartrate.
Crystal Properties Matthews coefficient Solvent content 2.22 44.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.355 α = 90 b = 73.037 β = 93.97 c = 58.696 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 6M 2016-09-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.976300 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.598 45.69 98.8 0.04 0.999 14.95 3 57739 -3 31.266
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.598 1.64 96.2 0.756 0.484 1.46 2.86
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2JLQ 1.598 45.69 54856 2878 98.82 0.1634 0.1619 0.1734 0.1914 0.1981 RANDOM 26.389
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 0.08 -0.26 -0.3 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.403 r_dihedral_angle_4_deg 12.545 r_dihedral_angle_3_deg 11.787 r_dihedral_angle_1_deg 5.849 r_mcangle_it 2.573 r_mcbond_it 1.662 r_mcbond_other 1.637 r_angle_refined_deg 1.545 r_angle_other_deg 0.978 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.403 r_dihedral_angle_4_deg 12.545 r_dihedral_angle_3_deg 11.787 r_dihedral_angle_1_deg 5.849 r_mcangle_it 2.573 r_mcbond_it 1.662 r_mcbond_other 1.637 r_angle_refined_deg 1.545 r_angle_other_deg 0.978 r_chiral_restr 0.095 r_bond_refined_d 0.012 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3333 Nucleic Acid Atoms 92 Solvent Atoms 387 Heterogen Atoms 17
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction XSCALE data reduction XDS data scaling